rs201568246
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_022489.4(INF2):c.507+7G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0014 in 1,613,076 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_022489.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
INF2 | NM_022489.4 | c.507+7G>A | splice_region_variant, intron_variant | ENST00000392634.9 | |||
INF2 | NM_001031714.4 | c.507+7G>A | splice_region_variant, intron_variant | ||||
INF2 | NM_032714.3 | c.507+7G>A | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INF2 | ENST00000392634.9 | c.507+7G>A | splice_region_variant, intron_variant | 5 | NM_022489.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000900 AC: 137AN: 152196Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000929 AC: 231AN: 248558Hom.: 0 AF XY: 0.000873 AC XY: 118AN XY: 135220
GnomAD4 exome AF: 0.00145 AC: 2119AN: 1460762Hom.: 3 Cov.: 33 AF XY: 0.00138 AC XY: 1004AN XY: 726722
GnomAD4 genome ? AF: 0.000899 AC: 137AN: 152314Hom.: 0 Cov.: 34 AF XY: 0.000886 AC XY: 66AN XY: 74474
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | May 26, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2023 | INF2: BP4, BS1 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 30, 2018 | - - |
Focal segmental glomerulosclerosis 5;C4302667:Charcot-Marie-Tooth disease dominant intermediate E Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 28, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Sep 22, 2021 | - - |
Focal segmental glomerulosclerosis 5 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at